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Authors: Anastasios Tsaousis
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: Anastasios Tsaousis 2017. Flagellar transformation of Naegleria gruberi. protocols.io https://dx.doi.org/10.17504/protocols.io.hnhb5b6 Copy
Authors: Jacob Harris
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Alverson Lab
Summary: The FlowCam can be used to take quick cell density measurements of liquid samples.
Proper citation: Jacob Harris 2017. FlowCam Standard Operating Procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.hgjb3un Copy
Authors: Glen Wheeler, Colin Brownlee
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: A method to load algal cells with dextran-conjugated fluorescent dyes. This is a good way of testing and optimising conditions for biolistic DNA delivery.
Proper citation: Glen Wheeler, Colin Brownlee 2017. Biolistic dye loading protocol for marine phytoplankton. protocols.io https://dx.doi.org/10.17504/protocols.io.hpzb5p6 Copy
Authors: Mariana Rius, Joshua Rest
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab
Summary: Bioinformatic approach to identifying over-represented motifs in the region framing the start codon (25 bp up and downstream) for genes annotated in the three sequenced Labyrinthulomycete genomes (Aurantiochytrium limacinum, Schizochytrium aggregatum, and Aplanochytrium kergulense).
Proper citation: Mariana Rius, Joshua Rest 2017. Genome-wide Kozak Sequence Over-represented Motif Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.hikb4cw Copy
Authors: Jackie Collier
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab
Summary: Modified from one of the methods tested by Cox et al. 2009
Proper citation: Jackie Collier 2018. Cryopreservation of labyrinthulomycetes with DMSO and horse serum. protocols.io https://dx.doi.org/10.17504/protocols.io.pgudjww Copy
Authors: Aleksandra Kozyczkowska, Sebastian Najle, Eduard Ocaña-Pallarès, Cristina Aresté, Iñaki Ruiz-Trillo, Elena Casacuberta
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab, Emerging Organisms for Biology
Summary: This protocol describes the transfection of Corallochytrium limacisporum, one of the unicellular relatives of animals. The transfection is performed using Lonza Nucleofector System X and reporter cassettes that contain endogenous regulatory elements of C. limacisporum.
Proper citation: Aleksandra Kozyczkowska, Sebastian Najle, Eduard Ocaña-Pallarès, Cristina Aresté, Iñaki Ruiz-Trillo, Elena Casacuberta 2020. Stable transfection of unicellular relative of animals, Corallochytrium limacisporum, using Lonza Nucleofector. protocols.io https://dx.doi.org/10.17504/protocols.io.bpfgmjjw Copy
Authors: Fatma Gomaa, Roberto Docampo, Virginia Edgcomb, Peter Girguis, Zuhong Li
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: Fatma Gomaa, Roberto Docampo, Virginia Edgcomb, Peter Girguis, Zuhong Li 2018. Bodo saltans tagging plasmid: 69 kDa paraflagellar rod protein 2C cassette for C terminal tagging_BsTub. protocols.io https://dx.doi.org/10.17504/protocols.io.s5peg5n Copy
Authors: This protocol modified from: Pandey A, Bhathena Z. 2014. Prevalence of PUFA Rich Thraustochytrids sps. along the Coast of Mumbai for Produ
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab
Summary: This protocol modified from: Pandey A, Bhathena Z. 2014. Prevalence of PUFA Rich Thraustochytrids sps. along the
Coast of Mumbai for Production of Bio Oil. Journal of Food and Nutrition
Research 2(12): 993-999.
Proper citation: This protocol modified from: Pandey A, Bhathena Z. 2014. Prevalence of PUFA Rich Thraustochytrids sps. along the Coast of Mumbai for Produ 2017. Staining Unfixed Labyrinthulomycetes with Nile Red. protocols.io https://dx.doi.org/10.17504/protocols.io.hghb3t6 Copy
Authors: Elena Casacuberta, Aleksandra Kozyczkowska, Sebastian Najle
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab, Emerging Organisms for Biology
Summary: This is a protocol for transient transfection of the Icthyosporean Abeoforma whisleri. This protocol has an efficiency of 1-2% calculated from fluorescent positive cell from Flow Cytometry data, using the amount of cells and DNA described in the protocol. Increasing DNA from above 1 microgram/microliter does not increase transfection.
Proper citation: Elena Casacuberta, Aleksandra Kozyczkowska, Sebastian Najle 2019. Abeoforma whisleri transient transfection protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.zexf3fn Copy
Authors: Natalia Wandyszewska and Anna Vanclova
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: This protocol we have used for the electroporation of mRNA encoding reporter gene Lucipherase into following organisms: Chromera velia, Alexandrium minutum, Euglena gracilis, Pyramimonas parkease, Pyramimonas orientalis, Eutreptiella gymnastica, Pseudonitzschia multiseries and Trichomonas vaginalis (a control). In any case we have not detected a specific lucipharease activity.
Proper citation: Natalia Wandyszewska and Anna Vanclova 2017. Protocols for mRNA electroporation. protocols.io https://dx.doi.org/10.17504/protocols.io.hh4b38w Copy
Authors: Daniel Richter, Parinaz Fozouni, Michael Eisen, Nicole King
Group: Ecology of Marine Plankton (ECOMAP) team - Roscoff, King Lab, Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: The origin of animals, which occurred over 600 million years ago, left no evidence in the fossil record. To trace the earliest events in animal prehistory, we compare extant animals to their closest living relatives, the choanoflagellates, in order to reconstruct the gene content of their last common ancestor and how it evolved on the stem lineage leading to animals. In this project, we increase the accuracy of ancestral animal and choanoflagellate gene content reconstructions by sequencing the transcriptomes of 19 species of choanoflagellates selected for their phylogenetic diversity.
Proper citation: Daniel Richter, Parinaz Fozouni, Michael Eisen, Nicole King 2017. Transcriptome sequencing of 19 diverse species of choanoflagellates. protocols.io https://dx.doi.org/10.17504/protocols.io.kwscxee Copy
Authors: Fatma Gomaa, Paulo A. Garcia, Jennifer Delany, Peter Girguis, Cullen R. Buie, and Virginia Edgcomb
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: Fatma Gomaa, Paulo A. Garcia, Jennifer Delany, Peter Girguis, Cullen R. Buie, and Virginia Edgcomb 2017. Genetic transformation of Parabodo caudatus using square wave electroporation system and pUB-GFP plasmid. protocols.io https://dx.doi.org/10.17504/protocols.io.hmeb43e Copy
Authors: Jernej Turnsek
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: This protocol was used to express a nourseothricin (nou/nat) resistance gene and a gene encoding a silaffin precursor TpSil3p-APEX2 fusion protein in Thalassiosira pseudonana (Tp) strain CCMP1335 using conjugation by largely following Karas et al. (2015). In addition to the protocol, I am listing some of my observations working with this diatom species. Please check the 'Before start' and 'Guidelines' sections for more information including a list of Tp episomes I've constructed and which are available upon request. For additional background on my overacrching experimental aim, please refer to this document. 1. E. V. Armbrust, The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism. Science. 306, 79–86 (2004).2. B. J. Karas et al., Designer diatom episomes delivered by bacterial conjugation. Nat. Commun. 6, 6925 (2015).Keeping in mind that diatom episomes contain a yeast centromere, it would be very interesting to see if conjugation could be adapted to organisms beyond diatoms.
Proper citation: Jernej Turnsek 2016. Conjugation of Thalassiosira pseudonana. protocols.io https://dx.doi.org/10.17504/protocols.io.f55bq86 Copy
Authors: Pia Elustondo
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Slamovits Lab
Proper citation: Pia Elustondo 2017. Calcium phosphate transfection of Oxyrrhis marina with an Alexa488-labelled DNA fragment. protocols.io https://dx.doi.org/10.17504/protocols.io.ha4b2gw Copy
Authors: Francois-Yves bouget
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: This protocol describes the selection and growth of stable transformants in semi solid agarose medium. Developped initially for Ostreococcus tauri, it also works for Bathycoccus.
Proper citation: Francois-Yves bouget 2017. Selection of stable transformants in Ostreococcus tauri and Bathycoccus prasinos. protocols.io https://dx.doi.org/10.17504/protocols.io.hddb226 Copy
Authors: Imen Lassadi
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: Imen Lassadi 2017. Glass beads-based transformation protocol for Perkinsus marinus. protocols.io https://dx.doi.org/10.17504/protocols.io.g36byre Copy
Authors: RACHELE CESARONI, Rachele Cesaroni
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: RACHELE CESARONI, Rachele Cesaroni 2019. Euplotes crassus transfection using FuGene HD Transfection Reagent as vehicle (provisional). protocols.io https://dx.doi.org/10.17504/protocols.io.2apgadn Copy
Authors: Lu Wang, Brittany Sprecher, Huan Zhang, Senjie Lin
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: Protocol of dinoflagellate cell transformation
Proper citation: Lu Wang, Brittany Sprecher, Huan Zhang, Senjie Lin 2019. Dinoflagellate transformation. protocols.io https://dx.doi.org/10.17504/protocols.io.7prhmm6 Copy
Authors: Lev Tsypin, Aaron Turkewitz
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: This protocol describes how we grew S. robusta and stored cultures at 4 C. Under these condtiions, the cells grow to a maximum density of 2-2.5 x 106 cells/mL.
Proper citation: Lev Tsypin, Aaron Turkewitz 2019. Cultivation of Seminavis robusta. protocols.io https://dx.doi.org/10.17504/protocols.io.337gqrn Copy
Authors: Glen Wheeler, Rowena Stern
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: Glen Wheeler, Rowena Stern 2019. Biolistic transformation of Isochrysis galbana. protocols.io https://dx.doi.org/10.17504/protocols.io.2pugdnw Copy
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